Browsing by Subject "SYSTEMATICS"

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  • Young, Andrew Donovan; Lemmon, Alan R.; Skevington, Jeffrey H.; Mengual, Ximo; Ståhls, Gunilla; Reemer, Menno; Jordaens, Kurt; Kelso, Scott; Lemmon, Emily Moriarty; Hauser, Martin; De Meyer, Marc; Misof, Bernhard; Wiegmann, Brian M. (2016)
    Background: Anchored hybrid enrichment is a form of next-generation sequencing that uses oligonucleotide probes to target conserved regions of the genome flanked by less conserved regions in order to acquire data useful for phylogenetic inference from a broad range of taxa. Once a probe kit is developed, anchored hybrid enrichment is superior to traditional PCR-based Sanger sequencing in terms of both the amount of genomic data that can be recovered and effective cost. Due to their incredibly diverse nature, importance as pollinators, and historical instability with regard to subfamilial and tribal classification, Syrphidae (flower flies or hoverflies) are an ideal candidate for anchored hybrid enrichment-based phylogenetics, especially since recent molecular phylogenies of the syrphids using only a few markers have resulted in highly unresolved topologies. Over 6200 syrphids are currently known and uncovering their phylogeny will help us to understand how these species have diversified, providing insight into an array of ecological processes, from the development of adult mimicry, the origin of adult migration, to pollination patterns and the evolution of larval resource utilization. Results: We present the first use of anchored hybrid enrichment in insect phylogenetics on a dataset containing 30 flower fly species from across all four subfamilies and 11 tribes out of 15. To produce a phylogenetic hypothesis, 559 loci were sampled to produce a final dataset containing 217,702 sites. We recovered a well resolved topology with bootstrap support values that were almost universally >95 %. The subfamily Eristalinae is recovered as paraphyletic, with the strongest support for this hypothesis to date. The ant predators in the Microdontinae are sister to all other syrphids. Syrphinae and Pipizinae are monophyletic and sister to each other. Larval predation on soft-bodied hemipterans evolved only once in this family. Conclusions: Anchored hybrid enrichment was successful in producing a robustly supported phylogenetic hypothesis for the syrphids. Subfamilial reconstruction is concordant with recent phylogenetic hypotheses, but with much higher support values. With the newly designed probe kit this analysis could be rapidly expanded with further sampling, opening the door to more comprehensive analyses targeting problem areas in syrphid phylogenetics and ecology.
  • Acanski, Jelena; Vujic, Ante; Djan, Mihajla; Obreht Vidakovic, Dragana; Ståhls, Gunilla; Radenkovic, Snezana (2016)
    Several recent studies have detected and described complexes of cryptic and sibling species in the genus Merodon (Diptera, Syrphidae). One representative of these complexes is the Merodon avidus complex that contains four sibling species, which have proven difficult to distinguish using traditional morphological characters. In the present study, we use two geometric morphometric approaches, as well as molecular characters of the 5' -end of the mtDNA COI gene, to delimit sibling taxa. Analyses based on these data were used to strengthen species boundaries within the complex, and to validate the status of a previously-recognized cryptic taxon from Lesvos Island (Greece), here described as Merodon megavidus Vujic & Radenkovic sp. nov. Geometric morphometric results of both wing and surstylus shape confirm the present classification for three sibling species-M. avidus (Rossi, 1790), M. moenium Wiedemann in Meigen, 1822 and M. ibericus Vujic, 2015-and, importantly, clearly discriminate the newly-described taxon Merodon megavidus sp. nov. In addition to our geometric morphometric results, supporting characters were obtained from molecular analyses of mtDNA COI sequences, which clearly differentiated M. megavidus sp. nov. from the other members of the M. avidus complex. Molecular analyses revealed that the earliest divergence of M. ibericus occurred around 800 ky BP, while the most recent separation happened between M. avidus and M. moenium around 87 ky BP.
  • Biffignandi, Gherard Batisti; Gibbon, Marjorie J.; Corbella, Marta; Thorpe, Harry A.; Merla, Cristina; Castelli, Michele; Kallonen, Teemu; Pegrum, Katie; Brisse, Sylvain; Corander, Jukka; Marone, Piero; Feil, Edward J.; Sassera, Davide (2021)
    During a citywide microbiological screening project in Pavia (Italy) a bacterial strain isolated from the surface of an Automated Teller Machine was classified as a Klebsiella sp. by MALDI-TOF spectrometry, and shown to be susceptible to the most antimicrobial classes by phenotypic testing. After Illumina genome sequencing and subsequent assembly, a high-quality draft genome was obtained (size = 5,051,593 bp, N50=615,571 bp, largest contig = 1,328,029 bp, N_contig = 17, GC content = 51.58%, coverage= 141.42), absence of antimicrobial resistance genes was confirmed, but the strain resulted to be highly divergent from all Klebsiella, and more related to other Enterobacteriaceae. The higher values of 16S rRNA identity were with members of the genera Citrobacter, Salmonella, and "Superficieibacter." An ortholog-based phylogenomic analysis indicated a sister group relationship with "Superficieibacter electus," in a distinct Glade from other members of the Enterobacteriaceae family. In order to evaluate whether the novel genome represents a new species of "Superficiebacter," average nucleotide identity (ANI) and Hadamard analysis were performed on a dataset of 78 Enterobacteriaceae. The novel genome showed an ANI of 87.51% with S. electus, which compared on identity values between other members of the family, clearly indicates that the genome represents a new species within the genus "Superficieibacter." We propose for the new species the name "Superficieibacter maynardsmithii."
  • Simões, Carlynne C.; Cerqueira, Pablo Vieira; Peloso, Pedro; Aleixo, Alexandre (2022)
    Integrative taxonomic studies continue to reveal that many current polytypic species of birds are in fact constituted by two or more species and therefore have been central in uncovering 'hidden' or 'cryptic' biodiversity. The Olivaceous Flatbill (Aves: Tyrannidae: Rhynchocyclus olivaceus) currently has nine recognized subspecies distributed throughout the Neotropics, but so far, no complete phylogenetic hypothesis exists to test the validity and evolutionary relationships among them. To remedy this, we conducted a multi-character integrative taxonomic revision of the genus Rhynchocyclus, focusing on the polytypic R. olivaceus. The combination of a taxonomically dense sampled multilocus phylogeny (including three mitochondrial and two nuclear genes) with phenotypic analyses including morphological and vocal characters pointed to several taxonomic inconsistencies within R. olivaceus. The analyses strongly support that R. olivaceus is paraphyletic, with an exclusively cis-Andean clade (where the topotypic R. olivaceus is found) clustering as sister to Rhynchocyclus fulvipectus, to the exclusion of a clade grouping trans-Andean and western Amazonian populations currently placed in R. olivaceus-one of which is unnamed and fully diagnosable based on vocal and genetic characters. Consistent with the phylogenetic results, our vocal analyses identified at least four morphologically cryptic lineages within R. olivaceus that can be mutually diagnosed from each other by different loudsongs and call parameters. Therefore, we provide evidence for splitting these four groups into separate species, two of which are sympatric but not syntopic in western Amazonia, including an unnamed species described herein-Rhynchocyclus cryptus, sp. nov.
  • Acanski, Jelena; Vujic, Ante; Sasic Zoric, Ljiljana; Radenkovi, Snezana; Markov, Zlata; Ståhls, Gunilla (2022)
    In this study, we examined the morphology, genetics and distribution of the members of the Merodon chalybeus subgroup (M. aureus species group): M. chalybeus Wiedemann in Meigen, 1822, M. minutus Strobl, 1893 and M. robustus Veselić, Vujić & Radenković, 2017. Two of the species, M. chalybeus and M. minutus, are morphologically very similar and often misidentified in the literature. Here, by employing an integrative taxonomic approach we provide strong evidence for the separation of M. chalybeus and M. minutus. Our results show their clear allopatric distribution: M. minutus on the Balkan Peninsula, Sicily, Sardinia and Corsica, while M. chalybeus is a western Mediterranean species distributed on the Iberian Peninsula and northwest Africa. Data on the distribution of M. robustus were updated, with new records from Cyprus, Israel and Turkey, besides its type locality (Samos in Greece). We provide evidence for M. chalybeus and M. minutus representing a species complex, named the M. chalybeus complex, which together with M. robustus constitute the M. chalybeus subgroup.
  • Murillo Ramos, Leidys Del Carmen; Chazot, Nicolas; Sihvonen, Pasi; Õunap, Erki; Jiang, Nan; Han, Hongxiang; Clarke, John T.; Davis, Robert B.; Tammaru, Toomas; Wahlberg, Niklas (2021)
    Understanding how and why some groups have become more species-rich than others, and how past biogeography may have shaped their current distribution, are questions that evolutionary biologists have long attempted to answer. We investigated diversification patterns and historical biogeography of a hyperdiverse lineage of Lepidoptera, the geometrid moths, by studying its most species-rich tribe Boarmiini, which comprises ca. 200 genera and ca. known 3000 species. We inferred the evolutionary relationships of Boarmiini based on a dataset of 346 taxa, with up to eight genetic markers under a maximum likelihood approach. The monophyly of Boarmiiniis strongly supported. However, the phylogenetic position of many taxa does not agree with current taxonomy, although the monophyly of most major genera within the tribe is supported after minor adjustments. Three genera are synonymized, one new combination is proposed, and four species are placed in incertae sedis within Boarmiini. Our results support the idea of a rapid initial diversification of Boarmiini, which also implies that no major taxonomic subdivisions of the group can currently be proposed. A time-calibrated tree and biogeographical analyses suggest that boarmiines appeared in Laurasia ca. 52 Mya, followed by dispersal events throughout the Australasian, African and Neotropical regions. Most of the transcontinental dispersal events occurred in the Eocene, a period of intense geological activity and rapid climate change. Diversification analyses showed a relatively constant diversification rate for all Boarmiini, except in one clade containing the species-rich genus Cleora. The present work represents a substantial contribution towards understanding the evolutionary origin of Boarmiini moths. Our results, inevitably biased by taxon sampling, highlight the difficulties with working on species-rich groups that have not received much attention outside of Europe. Specifically, poor knowledge of the natural history of geometrids (particularly in tropical clades) limits our ability to identify key innovations underlying the diversification of boarmiines.
  • Cardueae Radiations Grp (2019)
    Classification of tribe Cardueae in natural subtribes has always been a challenge due to the lack of support of some critical branches in previous phylogenies based on traditional Sanger markers. With the aim to propose a new subtribal delimitation, we applied a Hyb-Seq approach to a set of 76 Cardueae species representing all subtribes and informal groups defined in the tribe, targeting 1061 nuclear conserved orthology loci (COS) designed for Compositae and obtaining chloroplast coding regions as by-product of off-target reads. For the extraction of the target nuclear data, we used two strategies, PHYLUCE and HybPiper, and 776 and 1055 COS loci were recovered with each of them, respectively. Additionally, 87 chloroplast genes were assembled and annotated. With three datasets, phylogenetic relationships were reconstructed using both concatenation and coalescent approaches. Phylogenetic analyses of the nuclear datasets fully resolved virtually all nodes with very high support. Nuclear and plastid tree topologies are mostly congruent with a very limited number of incongruent nodes. Based on the well-solved phylogenies obtained, we propose a new taxonomic scheme of 12 monophyletic and morphologically consistent subtribes: Carlininae, Cardopatiinae, Echinopsinae, Dipterocominae (new), Xerantheminae (new), Berardiinae (new), Staehelininae (new), Onopordinae (new), Carduinae (redelimited), Arctiinae (new), Saussureinae (new), and Centaureinae. In addition, we further updated the temporal framework for origin and diversification of these subtribes. Our results highlight the power of Hyb-Seq over Sanger sequencing of a few DNA markers in solving phylogenetic relationships of traditionally difficult groups.
  • Bravo, Gustavo A.; Whitney, Bret M.; Belmonte-Lopes, Ricardo; Bornschein, Marcos R.; Aristizabal, Natalia; Beco, Renata; Battilana, Jaqueline; Naka, Luciano N.; Aleixo, Alexandre; Pie, Marcio R.; Silveira, Luis F.; Derryberry, Elizabeth P.; Brumfield, Robb T. (2021)
    The family Thamnophilidae is a species-rich Neotropical radiation of passerine birds. Current classification of its 235 species is mostly based on morphological similarities, but recent studies integrating comprehensive phenotypic and phylogenetic data have redefined taxonomic limits of several taxa. Here, we assess generic relationships of Herpsilochmus, Sakesphorus, Thamnophilus, Biatas, and Dysithamnus using DNA sequences from the mitochondrion, nuclear exons, and ultraconserved elements, with further attention to interspecific relationships within Herpsilochmus. We show that Herpsilochmus and Sakesphorus are not monophyletic. We resolve Herpsilochmus sellowi as a deep-branch sister to the monotypic genus Biatas and Sakesphorus cristatus as sister to a clade comprising Herpsilochmus sensu stricto and Dysithamnus. These results are consistent across loci, obtained via concatenation and coalescent-based analyses, and supported by likelihood-ratio tests of the distribution of our sampled coalescent histories. The phenotypic distinctiveness of both H. sellowi and Biatas argues against merging them into a single genus. Because no generic name is available for H. sellowi, we describe a monotypic genus. The polyphyly of Sakesphorus warrants recognition of the available generic name Sakesphoroides for the distinctive and monotypic S. cristatus. Furthermore, we recover 6 well-supported species groups within Herpsilochmus sensu stricto. Within the context of the family as a whole, the ubiquity of long terminal branches representing monotypic genera points to extinction events among ancestors of these lineages. We suggest that retention of ancestral characters or random genetic drift coupled with extensive extinction could explain the high degree of morphological and ecological similarity across these taxa, but we highlight the potential role of the environment in driving adaptive phenotypic convergence. Finally, our results send a cautionary message against the blind use of phylogenies containing imputed data based on taxonomy due to the increasingly frequent mismatches between traditional taxonomic classification and molecular phylogenies.
  • Milano, Filippo; Borio, Luca; Komposch, Christian; Mammola, Stefano; Pantini, Paolo; Pavlek, Martina; Isaia, Marco (2022)
    Background The genus Troglohyphantes Joseph, 1882 (Araneae, Linyphiidae) includes 131 species, mainly distributed across the main European mountain ranges. The Alps and the north-western Dinarides account for 66 species, most of them showing narrow or even point-like distributions. The majority of Troglohyphantes spiders dwell in subterranean habitats including caves, mines, soil litter, rocky debris and other moist and shaded retreats. Despite being intensively studied from taxonomic, ecological and biogeographic standpoints, knowledge on the status of conservation and on the potential risk of extinction of these spiders is lagging. To date, only three species have been included in the global IUCN Red List, but their status has not been updated ever since their last assessment in 1996. The aim of this contribution is to assess the Alpine and north-western Dinaric species of the genus Troglohyphantes and to re-assess the species previously evaluated, according to the last version of the IUCN Red List Categories and Criteria. New information Amongst the 66 species here considered, 62 had sufficient data to allow the quantification of their Extent Of Occurrence (EOO) and Area Of Occupancy (AOO). Most of the species have a narrow distribution range, with an estimated EOO < 20,000 km2 and AOO < 2,000 km2, meeting the thresholds for the inclusion in the threatened categories. Five species have a more widespread distribution (EOO > 20,000 km2), extending across multiple countries. The quality of the data on distribution of four species was not sufficient to provide a reliable estimation of the distribution range. A continuing decline in EOO, AOO and habitat quality was inferred for 30 species. The majority of them were subterranean specialised species, with a reduced thermal tolerance and a low dispersal ability. Accordingly, changes in subterranean microclimatic conditions due to climate change represent a major threat for these species. Land-use change and habitat alteration were identified as additional relevant threats for several species. A considerable proportion of the species here assessed was found in protected areas and in sites of the Natura 2000 network. In addition, 14 species are formally protected by national and sub-national legislation. At present, 25 species are listed in the regional Red Lists. Long-term monitoring programmes, management plans for both the species and their habitats, expansion of the extant protected areas and designation of new ones, should be considered as the most effective approaches to species conservation.
  • Hill, Jason; Rastas, Pasi; Hornett, Emily A.; Neethiraj, Ramprasad; Clark, Nathan; Morehouse, Nathan; Celorio-Mancera, Maria De La Paz; Carnicer, Jofre; Dircksen, Heinrich; Meslin, Camille; Keehnen, Naomi; Pruisscher, Peter; Sikkink, Kristin; Vives, Maria; Vogel, Heiko; Wiklund, Christer; Woronik, Alyssa; Boggs, Carol L.; Nylin, Sören; Wheat, Christopher W. (2019)
    Chromosome evolution presents an enigma in the mega-diverse Lepidoptera. Most species exhibit constrained chromosome evolution with nearly identical haploid chromosome counts and chromosome-level gene collinearity among species more than 140 million years divergent. However, a few species possess radically inflated chromosomal counts due to extensive fission and fusion events. To address this enigma of constraint in the face of an exceptional ability to change, we investigated an unprecedented reorganization of the standard lepidopteran chromosome structure in the green-veined white butterfly (Pieris napi). We find that gene content in P. napi has been extensively rearranged in large collinear blocks, which until now have been masked by a haploid chromosome number close to the lepidopteran average. We observe that ancient chromosome ends have been maintained and collinear blocks are enriched for functionally related genes suggesting both a mechanism and a possible role for selection in determining the boundaries of these genome-wide rearrangements.